| Next changeset 1:86e36a2b44b0 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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qiime2__deblur__denoise_other.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 574ab3a299a9 qiime2__deblur__denoise_other.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__deblur__denoise_other.xml Mon Aug 29 19:25:44 2022 +0000 |
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| @@ -0,0 +1,93 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 deblur denoise-other" id="qiime2__deblur__denoise_other" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Deblur sequences using a user-specified positive filter.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version deblur</version_command> + <command detect_errors="aggressive">q2galaxy run deblur denoise_other '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> + <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> + <filter type="add_value" value="SampleData[SequencesWithQuality]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> + </param> + <param name="reference_seqs" type="data" format="qza" label="reference_seqs: FeatureData[Sequence]" help="[required] Positive filtering database. Keep all sequences aligning to these sequences."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Sequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> + </param> + <param name="trim_length" type="integer" value="" label="trim_length: Int" help="[required] Sequence trim length, specify -1 to disable trimming."/> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="left_trim_len" type="integer" min="0" value="0" label="left_trim_len: Int % Range(0, None)" help="[default: 0] Sequence trimming from the 5' end. A value of 0 will disable this trim."/> + <param name="sample_stats" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="sample_stats: Bool" help="[default: No] If true, gather stats per sample."/> + <param name="mean_error" type="float" value="0.005" label="mean_error: Float" help="[default: 0.005] The mean per nucleotide error, used for original sequence estimate."/> + <param name="indel_prob" type="float" value="0.01" label="indel_prob: Float" help="[default: 0.01] Insertion/deletion (indel) probability (same for N indels)."/> + <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/> + <param name="min_reads" type="integer" value="10" label="min_reads: Int" help="[default: 10] Retain only features appearing at least min_reads times across all samples in the resulting feature table."/> + <param name="min_size" type="integer" value="2" label="min_size: Int" help="[default: 2] In each sample, discard all features with an abundance less than min_size."/> + <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start: Int" help="[default: 1] Number of jobs to start (if to run in parallel)."/> + <param name="hashed_feature_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="hashed_feature_ids: Bool" help="[default: Yes] If true, hash the feature IDs."/> + </section> + </inputs> + <outputs> + <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> + <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> + <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: deblur denoise-other +============================= +Deblur sequences using a user-specified positive filter. + + +Outputs: +-------- +:table.qza: The resulting denoised feature table. +:representative_sequences.qza: The resulting feature sequences. +:stats.qza: Per-sample stats if requested. + +| + +Description: +------------ +Perform sequence quality control for Illumina data using the Deblur workflow, including positive alignment-based filtering. Only forward reads are supported at this time. This mode of execution is particularly useful when operating on non-16S data. For example, to apply Deblur to 18S data, you would want to specify a reference composed of 18S sequences in order to filter out sequences which do not appear to be 18S. The assessment is performed by local alignment using SortMeRNA with a permissive e-value threshold. + + +| + +</help> + <citations> + <citation type="bibtex">@article{cite1, + author = {Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob}, + journal = {MSystems}, + number = {2}, + pages = {e00191--16}, + publisher = {Am Soc Microbiol}, + title = {Deblur rapidly resolves single-nucleotide community sequence patterns}, + volume = {2}, + year = {2017} +} +</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> |